scholarly journals Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza

2021 ◽  
Author(s):  
Mahan Ghafari ◽  
Louis du Plessis ◽  
Jayna Raghwani ◽  
Samir Bhatt ◽  
Bo Xu ◽  
...  
Keyword(s):  
Growth Rates ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics ◽  
Disease Outbreaks ◽  
Purifying Selection ◽  
Evolutionary Rates ◽  
Logistic Growth ◽  
Time Dependency ◽  
Sampling Window ◽  
Over Time

High throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Here, we characterise the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and dataset sizes affects the accuracy of parameter estimation. We further use a generalised McDonald-Kreitman test to estimate the number of segregating non-neutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time-dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ~50% and ~100%, respectively, over the course of one year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time-dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2-4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating non-neutral sites, demonstrating the role of purifying selection in generating the time-dependency of evolutionary parameters during pandemics.

scholarly journals A NOTE ON ECONOMIC GROWTH WITH SUBSISTENCE CONSUMPTION

2010 ◽  
Vol 14 (5) ◽  
pp. 763-771 ◽  
Author(s):  
Holger Strulik
Keyword(s):  
Economic Growth ◽  
Growth Model ◽  
Growth Rates ◽  
Degree Of Freedom ◽  
Controversial Issue ◽  
Historical Evolution ◽  
Transitional Dynamics ◽  
Economic Growth Rates ◽  
Over Time ◽  
Savings Rates

It is well known that the performance of simple models of economic growth improves substantially through the introduction of subsistence consumption. How to compute subsistence needs, however, is a difficult and controversial issue. Here, I reconsider the linear (Ak) growth model with subsistence consumption and show that the evolution of savings rates and economic growth rates over time is independent of the size of subsistence needs. The model is thus more general and less subject to arbitrariness than might have been thought initially. Quantitatively, it is shown that, although there is no degree of freedom to manipulate transitional dynamics, the model approximates the historical evolution of savings rates and growth rates reasonably well.

scholarly journals Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

2012 ◽  
Vol 8 (4) ◽  
pp. e1002654 ◽  
Author(s):  
Frédéric Fabre ◽  
Josselin Montarry ◽  
Jérôme Coville ◽  
Rachid Senoussi ◽  
Vincent Simon ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

scholarly journals Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis

2021 ◽  
Author(s):  
William R. Shoemaker ◽  
Evgeniya Polezhaeva ◽  
Kenzie B. Givens ◽  
Jay T. Lennon
Keyword(s):  
Bacillus Subtilis ◽  
Molecular Evolution ◽  
Seed Bank ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Genetic Manipulation ◽  
Seed Banks ◽  
Rate Of Molecular Evolution ◽  
Over Time ◽  
Growth And Reproduction

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which in turn effects the evolution of their respective populations. Many organisms are able to respond to fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. We find that the ability to enter a dormant state increases the accumulation of genetic diversity over time and alters the trajectory of mutations, findings that are recapitulated using simulations based on a simple mathematical model. While the ability to form a seed bank does not alter the degree of negative selection, we find that it consistently alters the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank affects the direction and rate of molecular evolution over an extended evolutionary timescale.

scholarly journals Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4840 ◽  
Author(s):  
Kai Wei ◽  
Tingting Zhang ◽  
Lei Ma
Keyword(s):  
Active Sites ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Neutral Evolution ◽  
Structure Evolution ◽  
Tissue Cell ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

scholarly journals Longitudinal profiling of the lung microbiome in the AERIS study demonstrates repeatability of bacterial and eosinophilic COPD exacerbations

Thorax ◽  
2018 ◽  
Vol 73 (5) ◽  
pp. 422-430 ◽  
Author(s):  
David Mayhew ◽  
Nathalie Devos ◽  
Christophe Lambert ◽  
James R Brown ◽  
Stuart C Clarke ◽  
...  
Keyword(s):  
Disease Severity ◽  
High Throughput Sequencing ◽  
Respiratory Infections ◽  
Markov Chain Model ◽  
Chain Model ◽  
Copd Exacerbations ◽  
Lung Microbiome ◽  
Registration Number ◽  
The Stability ◽  
Over Time

BackgroundAlterations in the composition of the lung microbiome associated with adverse clinical outcomes, known as dysbiosis, have been implicated with disease severity and exacerbations in COPD.ObjectiveTo characterise longitudinal changes in the lung microbiome in the AERIS study (Acute Exacerbation and Respiratory InfectionS in COPD) and their relationship with associated COPD outcomes.MethodsWe surveyed 584 sputum samples from 101 patients with COPD to analyse the lung microbiome at both stable and exacerbation time points over 1 year using high-throughput sequencing of the 16S ribosomal RNA gene. We incorporated additional lung microbiology, blood markers and in-depth clinical assessments to classify COPD phenotypes.ResultsThe stability of the lung microbiome over time was more likely to be decreased in exacerbations and within individuals with higher exacerbation frequencies. Analysis of exacerbation phenotypes using a Markov chain model revealed that bacterial and eosinophilic exacerbations were more likely to be repeated in subsequent exacerbations within a subject, whereas viral exacerbations were not more likely to be repeated. We also confirmed the association of bacterial genera, including Haemophilus and Moraxella, with disease severity, exacerbation events and bronchiectasis.ConclusionsSubtypes of COPD have distinct bacterial compositions and stabilities over time. Some exacerbation subtypes have non-random probabilities of repeating those subtypes in the future. This study provides insights pertaining to the identification of bacterial targets in the lung and biomarkers to classify COPD subtypes and to determine appropriate treatments for the patient.Trial registration numberResults, NCT01360398.

scholarly journals Engraftment of rare, pathogenic donor hematopoietic mutations in unrelated hematopoietic stem cell transplantation

2020 ◽  
Vol 12 (526) ◽  
pp. eaax6249 ◽  
Author(s):  
Wing Hing Wong ◽  
Sima Bhatt ◽  
Kathryn Trinkaus ◽  
Iskra Pusic ◽  
Kevin Elliott ◽  
...  
Keyword(s):  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Cell Transplant ◽  
Younger Adults ◽  
Hematopoietic Stem ◽  
Clonal Hematopoiesis ◽  
Age Related ◽  
Over Time

Clonal hematopoiesis is associated with various age-related morbidities. Error-corrected sequencing (ECS) of human blood samples, with a limit of detection of ≥0.0001, has demonstrated that nearly every healthy individual >50 years old harbors rare hematopoietic clones below the detection limit of standard high-throughput sequencing. If these rare mutations confer survival or proliferation advantages, then the clone(s) could expand after a selective pressure such as chemotherapy, radiotherapy, or chronic immunosuppression. Given these observations and the lack of quantitative data regarding clonal hematopoiesis in adolescents and young adults, who are more likely to serve as unrelated hematopoietic stem cell donors, we completed this pilot study to determine whether younger adults harbored hematopoietic clones with pathogenic mutations, how often those clones were transferred to recipients, and what happened to these clones over time after transplantation. We performed ECS on 125 blood and marrow samples from 25 matched unrelated donors and recipients. Clonal mutations, with a median variant allele frequency of 0.00247, were found in 11 donors (44%; median, 36 years old). Of the mutated clones, 84.2% of mutations were predicted to be molecularly pathogenic and 100% engrafted in recipients. Recipients also demonstrated de novo clonal expansion within the first 100 days after hematopoietic stem cell transplant (HSCT). Given this pilot demonstration that rare, pathogenic clonal mutations are far more prevalent in younger adults than previously appreciated, and they engraft in recipients and persist over time, larger studies with longer follow-up are necessary to correlate clonal engraftment with post-HSCT morbidity.

Evolution of behavioral resistance in host-pathogen systems

2020 ◽  
Author(s):  
Caroline R. Amoroso ◽  
Janis Antonovics
Keyword(s):  
Social Interactions ◽  
Evolutionary Dynamics ◽  
Disease Risk ◽  
Disease Outbreaks ◽  
Mixed Strategies ◽  
Costs And Benefits ◽  
Parasite Resistance ◽  
Costs Of Disease ◽  
Physiological Resistance ◽  
Behavioral Resistance

AbstractBehavioral resistance to parasites is widespread in animals, yet little is known about the evolutionary dynamics that have shaped these strategies. We show that theory developed for the evolution of physiological parasite resistance can only be applied to behavioral resistance under limited circumstances. We find that accounting explicitly for the behavioral processes, including the detectability of infected individuals, leads to novel dynamics that are strongly dependent on the nature of the costs and benefits of social interactions. As with physiological resistance, the evolutionary dynamics can also lead to mixed strategies that balance the costs of disease risk and the benefits of social interaction, with implications for understanding avoidance strategies in human disease outbreaks.

The Evolution of Bulged Areas in the Cylindrical Section of Coke Drums

2019 ◽  
Author(s):  
Egler Araque ◽  
Darren Love ◽  
Stephen Park ◽  
Daryl Rutt ◽  
Armando Moret Tapia ◽  
...  
Keyword(s):  
Growth Rates ◽  
Surface Damage ◽  
Cycle Times ◽  
Stress Cracking ◽  
Rates Of Change ◽  
Areas Of Concern ◽  
Observed Damage ◽  
The Relationship ◽  
Random Nature ◽  
Over Time

Abstract In recent years the understanding of the relationship between drum damage and bulge sharpness has improved significantly. The authors of this paper developed a new parameter called bulge sharpness and have previously shown the relationship between sharpness and observed damage. Further to this study, the authors have exhaustively studied the evolution of stress cracking (elephant skin) on mid-course bulges and have estimated the likelihood of finding a particular type of surface damage based on the observed sharpness levels. This correlation has led to a proposed scale to categorize stress cracking into three levels: minor, intermediate, and significant. In addition, the progression of bulge sharpness over time was analyzed and it was determined through statistical modeling that bulge sharpness can have a range of rates of change or sharpness growth rates: low, medium, and high. These sharpness growth rates were subsequently studied and their relationship with overall cycle times analyzed. The study also shows that individual coke drums can experience different sharpness growth rates and there can be a distribution of these rates. To determine when repairs should be conducted, coke drum operators must consider the expected operational run. While the random nature of coke drum damage can defy such targets, bulge sharpness growth assessments can be used to better define when repairs should be conducted. Understanding current bulge sharpness levels, year-over-year sharpness growth rates and their distribution, can significantly assist in targeting areas of concern for optimized repair strategies and can also be used to avoid unnecessary repairs.

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